add module for mykrobe predict and genotyphi parse (#1818)
* add module for mykrobe predict and genotyphi parse * Update meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>master
Robert A. Petit III
2 years ago
committed by
GitHub
parent
876bb807af
commit
6d6e3a018f
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process GENOTYPHI_PARSE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1':
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'quay.io/biocontainers/genotyphi:1.9.1--hdfd78af_1' }"
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input:
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tuple val(meta), path(json)
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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parse_typhi_mykrobe.py \\
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--jsons $json \\
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--prefix ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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genotyphi: \$(echo \$(genotyphi --version 2>&1) | sed 's/^.*GenoTyphi v//;' )
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END_VERSIONS
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"""
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}
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name: "genotyphi_parse"
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description: Genotype Salmonella Typhi from Mykrobe results
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keywords:
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- genotype
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- Salmonella Typhi
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tools:
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- "genotyphi":
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description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)"
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homepage: "https://github.com/katholt/genotyphi"
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documentation: "https://github.com/katholt/genotyphi"
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tool_dev_url: "https://github.com/katholt/genotyphi"
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doi: "https://github.com/katholt/genotyphi"
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licence: "['GPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- json:
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type: file
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description: JSON formatted file of Mykrobe results
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pattern: "*.json"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- tsv:
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type: file
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description: A tab-delimited file of predicted genotypes
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pattern: "*.tsv"
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authors:
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- "@rpetit3"
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process MYKROBE_PREDICT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1':
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'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }"
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input:
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tuple val(meta), path(seqs)
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val species
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output:
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tuple val(meta), path("${prefix}.csv") , emit: csv
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tuple val(meta), path("${prefix}.json"), emit: json
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mykrobe \\
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predict \\
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$args \\
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--species $species \\
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--threads $task.cpus \\
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--sample $prefix \\
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--format json_and_csv \\
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--output ${prefix} \\
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--seq $seqs
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mykrobe: \$(echo \$(mykrobe --version 2>&1) | sed 's/^.*mykrobe v//' )
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END_VERSIONS
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"""
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}
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name: "mykrobe_predict"
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description: AMR predictions for supported species
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keywords:
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- fastq
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- bam
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- antimicrobial resistance
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tools:
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- "mykrobe":
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description: "Antibiotic resistance prediction in minutes"
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homepage: "http://www.mykrobe.com/"
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documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
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tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
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doi: "10.1038/ncomms10063"
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licence: "['MIT']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- seqs:
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type: file
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description: BAM or FASTQ file
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pattern: "*.{bam,fastq.gz,fq.gz}"
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- species:
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type: string
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description: Species to make AMR prediction against
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- csv:
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type: file
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description: AMR predictions in CSV format
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pattern: "*.csv"
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- json:
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type: file
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description: AMR predictions in JSON format
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pattern: "*.json"
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authors:
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- "@rpetit3"
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
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include { GENOTYPHI_PARSE } from '../../../../modules/genotyphi/parse/main.nf'
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workflow test_mykrobe_predict {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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MYKROBE_PREDICT ( input, "typhi" )
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GENOTYPHI_PARSE ( MYKROBE_PREDICT.out.json )
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}
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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@ -0,0 +1,12 @@
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- name: genotyphi parse test_mykrobe_predict
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command: nextflow run ./tests/modules/genotyphi/parse -entry test_mykrobe_predict -c ./tests/config/nextflow.config -c ./tests/modules/genotyphi/parse/nextflow.config
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tags:
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- genotyphi/parse
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- genotyphi
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files:
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- path: output/genotyphi/test_predictResults.tsv
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contains: ["genome", "confidence", "supported", "test", "NA"]
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- path: output/mykrobe/test.csv
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contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
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- path: output/mykrobe/test.json
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contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
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workflow test_mykrobe_predict {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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MYKROBE_PREDICT ( input, "typhi" )
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}
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@ -0,0 +1,5 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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@ -0,0 +1,10 @@
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- name: mykrobe predict test_mykrobe_predict
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command: nextflow run ./tests/modules/mykrobe/predict -entry test_mykrobe_predict -c ./tests/config/nextflow.config -c ./tests/modules/mykrobe/predict/nextflow.config
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tags:
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- mykrobe/predict
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- mykrobe
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files:
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- path: output/mykrobe/test.csv
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contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
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- path: output/mykrobe/test.json
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contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
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